Yaamini’s Notebook: Pubathon 14 Day Plan

I’m going to get stuff done for Pubathon (I promise)!

After being productive in other ways for the past few months, I’m finally going to get my act together and really make some progress on Pubathon. Here are my 14-day plans for my metaanalysis and DNR papers:

C. gigas metaanalysis: My main goal over the next two weeks is to start analyzing data and write preliminary methods and introduction sections.

  • Monday, April 17: Start finding data, collating it and constructing a reference table
  • Tuesday, April 18: Find and collate data, construct a reference table
  • Wednesday, April 19: Find and collate data, construct a reference table
  • Thursday, April 20: Write data collection narrative in Methods
  • Friday, April 21: Create plan for data analysis
  • Monday, April 24: Start analyzing data
  • Tuesday, April 25: Analyze data, draft analysis narrative in Methods
  • Wednesday, April 26: Analyze data, start writing Introduction
  • Thursday, April 27: Anaylze data
  • Friday, April 28: Analyze data
  • Monday, May 1: Analyze data, refine Introduction

DNR Project:

  • Monday, April 17: Demultiplex data, send pecanpie inputs to Emma
  • Tuesday, April 18: Edit data analysis narrative in Methods, refine DIA analysis wiki
  • Wednesday, April 19: Add in placeholders for preliminary results, bullet point structure of results section
  • Thursday, April 20: Bullet point structure for Introduction section
  • Monday, April 24: Start writing Introduction section
  • Tuesday, April 25: Redo Skyline analyses with new .blib file (hopefully)?
  • Wednesday, April 26: Refine Methods section
  • Thursday, April 27: Refine Introduction section
  • Monday, May 1: Start writing Results narrative

from the responsible grad student http://ift.tt/2nWIOR1

Grace’s Notebook: Oly Histology Slides Thoughts

I took pictures of the tissues of a few histology slides from Laura’s O. lurida project.

Below are some thoughts I have on what we may be looking at using my past experience of looking at geoduck gonad histology, and using the histological work from two papers (Oates 2013 thesis) (Moore et al., 2016) found from a recent literature search on specifically O. lurida gonadal histology. Also, Brent came over and helped a lot. (Link to google drive folder)





Ones I’m unsure about:



Histology from Moore et al. 2016:



A P. asperdus annotation table:

Tab-delimited: http://d.pr/f/wISL

on SQLShare: https://sqlshare.uw.edu/detail/sr320/P_asperdus-bigtable_v03



Yaamini’s Notebook: Demultiplexing Update 2

Another new MSConvert CLI

Over the weekend, I was only able to convert 2 oyster .raw file, which can be found in this OWL folder. Austin figured out that another program, Prism, slows down after a given number of isolation windows. He rewrote our msconvert CLI, and Emma brought it over this morning.

Before we tried the new version, I shared the converted oyster1.mzML file with her so she can test it on pecanpie. Her notebook has the information for our test, which can be found here.

First, I unzipped the new version of msconvert under srlab » Documents » oystertest » oystertest2. I also made a copy of the config file and pasted it into oystertest2 (filename: config_fix.txt). I then ran the following code to convert oyster1.raw using the updated program.

 cd C:\Users\srlab\Documents\oystertest\oystertest2 msconvert.exe -c config_fix.txt 2017_January_23_envtstress_oyster1.raw  


Within minutes, the file finished converting! I uploaded to this OWL link.

I moved oyster1.raw to the folder oystertest » finished-raw. I then started converting the rest of my oyster .raw files.

 msconvert.exe -c config_fix.txt *.raw  


I’m going to check on the files over the course of the day, and will upload them to this OWL folder.

from the responsible grad student http://ift.tt/2nVJvdh